Apparatus and method for multiple reactions in small volumes

ABSTRACT

This describes an apparatus comprising a plate with a number of elements having a hydrophilic surface arranged in an array with an overlay having a hydrophobic surface. A height of the overlay is between about 5% and 100% of the diameter of the elements. The application also discloses a wall circumferential to the plate; and a removable grid insertable into the apparatus, said grid comprising dividers enclosing a number of through-holes, said through-holes spaced in the grid to allow alignment of the through-holes of the grid over the elements in the plate when said grid is inserted into the apparatus, said dividers of the grid inserted into the apparatus form sides of wells bottomed by the plate and at least one element on said plate.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a United States National Stage Application filedunder 35 U.S.C. § 371 of PCT Patent Application Serial No.PCT/SG2011/000263 filed on Jul. 25, 2011, which claims priority fromU.S. provisional patent application No. 61/367,049, filed Jul. 23, 2010,entitled, “Improved Handling and Use of Patterned Fluidic Array,” thedisclosure of which is incorporated herein, it its entirety, byreference.

BACKGROUND OF THE INVENTION

The invention generally relates generally to the fields of biology,chemistry, and biochemistry and, more particularly, to devices andmethods for performing multiple biological, biochemical, and chemicalassays in small volumes.

In the fields of biology, chemistry, and biochemistry, often subtlechanges to a molecule or a cell in a reaction can have consequences onthe results of reactions or assays using that molecule or cell. Forexample, changing a single amino acid (e.g., an alanine to a serine) ina polypeptide molecule or changing the growth conditions of a cell(e.g., growth in the presence of 10% fetal bovine serum versus 5% fetalbovine serum) can affect how the polypeptide or cell responds in a givenreaction (e.g., whether or not the polypeptide binds to a specificbinding agent or whether the cell responds to a growth factor).

Microtiter plates have been used for decades to enable the multiplereactions in small volume for applications including high-throughputscreening. For example, one commonly used immunological assay, theEnzyme-linked immunosorbent assay or “ELISA” can be used to determine ifa member of a binding agent/ligand pair is present in a sample, and, ifpresent, how much is present. For example, one member of the bindingagent/ligand pair (e.g., an antibody) can be immobilized to the bottomof the multiple wells on a microtiter plate (e.g., through non-specificadsorption of the antibody into the wells of the plate), and thenmultiple samples can be assessed as to the presence and/or concentrationof the antibody's specific ligand by adding each different sample to oneof the wells of the microtiter plate and then detecting binding of thesample to the well (e.g., using a detectably labeled antibody specificfor the ligand).

Standard microtiter plates are commercially available from numerousmanufacturers (e.g., Thermo Fisher Scientific, Waltham, Mass.) and canbe made from numerous different materials (see, e.g., Bouche, F B etal., Clinical Chemistry 48: 378, 380, 2002). However, standardmicrotiter plates have several limitations. Most relevantly, they arelimited by the number of wells on the plate. To increase the number ofreactions that can be run (e.g., increase the number of samples that canbe tested at the same time), the number of wells on a single plate canvary from 6 wells to 1536 wells per plate.

Recently, in the field of biology and biochemistry, DNA microarrays andprotein microarrays have been employed to increase still further thenumber of different reactions that can be performed simultaneously. DNAmicroarrays are made by adhering DNA probes (e.g., single-strandedprobes) to the surface of a chip or slide (e.g., made of glass orsilicon) in an array of dots or spots. Different samples of DNA are thenadded to each of the spots and screened for the ability to bind thespots (e.g., through hybridization of a nucleic acid in the sample tothe surface-bound probe). Detection of binding can then be made, forexample, by fluorescent or chemical means (which, in some cases, ispreceded by amplification of the bound nucleic acid molecules to enhancedetection). DNA microarray technology is well known (see, e.g., U.S.Pat. Nos. 5,700,637; 7,323,555; 6,862,363; 7,414,117; and 7,359,537).

Of course there are some fundamental differences between microarrays andmicrotiter plates. In microtiter plates, a reaction in an individualwell can be carried out independently regardless of a reaction in theneighboring wells. In contrast, the active spots (similar to ‘wells’ ofa microtiter plate) in microarrays are usually exposed to a commonsolution. Unlike micrrotiter plates, microarrays do not offer anycapability where an individual spot can be exposed to a differentsolution during a repeated process of addition, incubation, and washing.

Protein arrays on glass slides have also been described (see Arenkov etal., Anal. Biochem 278: 123-131, 2000; Guschin et al., Anal. Biochem.250: 202-211, 1997; MacBeath and Schreiber, Science 289: 1760-1763,2000) as well as protein arrays on microwell or nanowell chips (see Zhuand Snyder, Curr. Opin. Chem. Biol. 5(1):40-45, 2001). However, inaddition to having the same limitations as DNA microarrays, proteinarrays have additional challenged. For example, complex chemicals, suchas proteins and other non-nucleic acid biological molecules (e.g., fattyacids and carbohydrates), are more difficult to use in microarrays formultiple reactions. This is due a variety of actors including, forexample, the storage and binding requirements of the molecules (e.g.,storage may be preferable at −20° C. while binding may be preferable at37° C. For these reasons, protein microarrays are generally lessspecific than assays such as ELISAs that use microtiter plates.

Accordingly, there is a need find a solution for running multiplereactions that can combine the specificity of microtiter plate assayswith the microarray's increased number of reactions that can be inmultiple.

BRIEF SUMMARY OF THE INVENTION

The various embodiments of the invention are based on the discovery of asystem that combines the advantages of a standard microtiter plate withthe advantages of a flat microarray. The various aspect of theinvention, thus, facilitates multiple reactions (e.g., involvingmolecules and/or living cells) in small volumes.

Accordingly, in a first aspect, the invention provides a systemcomprising: an apparatus comprising: a plate comprising a number ofelements having a first surface energy arranged in an array with anoverlay having a second surface energy, and a wall circumferential tothe plate; and a removable grid insertable into the apparatus to bepositioned over the plate and within the wall of the apparatus, saidgrid comprising dividers enclosing a number of through-holes, saidthrough-holes spaced in the grid to allow alignment of the through-holesof the grid over the elements in the plate when said grid is insertedinto the apparatus, wherein said dividers of the grid inserted into theapparatus form sides of wells bottomed by the plate and at least oneelement on said plate.

In another aspect, the invention provides a removable grid insertableinto an apparatus comprising a plate comprising a number of elementshaving a first surface energy arranged in an array with an overlayhaving a second surface energy and a wall circumferential to the plate,said grid comprising dividers enclosing a number of through-holes, saidthrough-holes spaced in the grid to allow alignment of the through-holesof the grid over the elements in the plate when said grid is insertedinto the apparatus, wherein said dividers of the grid inserted into theapparatus form sides of wells bottomed by the plate and at least oneelement on said plate.

In some embodiments, the apparatus further comprises a positioningstructure adjacent to the interior of the wall so as to guide alignmentof the through-holes of the grid over the elements when the grid isinserted into the apparatus. In various embodiments, the number ofthrough-holes in the grid is the same as or is smaller than the numberof elements in the plate. In some embodiments, each through-hole isaligned over a single element in the plate. In some embodiments, eachthrough-hole is aligned over multiple elements in the plate.

In some embodiments, the first surface energy results in a hydrophilicsurface. In some embodiments, the second surface energy results in ahydrophobic surface. In some embodiments, the grid has a second surfaceenergy.

In further embodiments, the grid further comprises offsetting featureson the surface of the grid that touches the plate when the grid isinserted into the apparatus. In some embodiments, the grid furthercomprises at least one structure on the surface of the grid that doesnot touch the plate when the grid is inserted into the apparatus, saidstructure sized for a user (e.g., a human or an automated device) tograb the grid and insert or remove the grid from the apparatus. In someembodiments, the grid further comprises a reservoir encompassing atleast one through-hole of the grid, said reservoir on the surface of thegrid that does not touch the plate when the grid is inserted into theapparatus.

In various embodiments, the dividers of the grid and the wall of theapparatus are of the same height. In some embodiments, the dividers ofthe grid are of a height that is higher than the height of the wall ofthe apparatus.

In various embodiments, the grid further comprises a plane perpendicularto the dividers of the grid attached to the surface of the grid thatdoes not touch the plate when the grid is inserted into the apparatus,wherein the plane covers all of the through-holes of the grid. Invarious embodiments, the plane further comprises side planesperpendicular to said plane, said side planes parallel to and shorter inheight than the dividers of the grid. In some embodiments, the gridfurther comprises offsetting features between the dividers and theplane.

In another aspect, the invention provides a method for performingmultiple reactions (e.g., at the same time). The method includes (a)providing a system comprising (i) an apparatus comprising a platecomprising a number of elements having a first surface energy arrangedin an array with an overlay having a second surface energy and a wallcircumferential to the plate and (ii) a removable grid insertable intothe apparatus to be positioned over the plate and within the wall of theapparatus, said grid comprising dividers enclosing a number ofthrough-holes, said through-holes spaced in the grid to allow alignmentof the through-holes of the grid over the elements in the plate whensaid grid is inserted into the apparatus, wherein said dividers of saidinserted grid form wells bottomed by the plate and at least one elementon said plate; (b) adding a first reagent-containing liquid through thethrough-holes of the grid of the system under conditions where the firstreagent in the liquid adheres to the elements on the plate; (c) addingrinsing oil to said plate in an amount necessary to cover said plate;(d) draining excess rinsing oil from the plate resulting from step (c);(e) adding a liquid through the through-holes of the grid of the system,said liquid containing a second reagent suspected of reacting with thefirst reagent; (f) removing the grid from the apparatus; (g) washing theapparatus; and (h) detecting reaction of the second reagent with thefirst reagent. In some embodiments, the method further comprisesinserting the grid into the apparatus following step (g). In someembodiments, step (h) is performed using a third reagent (e.g., adetectably labeled third reagent). In some embodiments, the thirdreagent is borne in a liquid.

In another aspect, the invention provides a method for performingmultiple reactions (e.g., at the same time). The method includes (a)providing a system comprising (i) an apparatus comprising a platecomprising a number of elements having a first surface energy arrangedin an array with an overlay having a second surface energy and a wallcircumferential to the plate and (ii) a removable grid insertable intothe apparatus to be positioned over the plate and within the wall of theapparatus, said grid comprising dividers enclosing a number ofthrough-holes, said through-holes spaced in the grid to allow alignmentof the through-holes of the grid over the elements in the plate whensaid grid is inserted into the apparatus, wherein said dividers of saidinserted grid form wells bottomed by the plate and at least one elementon said plate; (b) adding a first reagent-containing liquid through thethrough-holes of the grid of the system under conditions where the firstreagent in the liquid adheres to the elements on the plate; (c) adding aliquid through the through-holes of the grid of the system, said liquidcontaining a second reagent suspected of reacting with the firstreagent; (d) removing the grid from the apparatus; (e) washing theapparatus; and (f) detecting reaction of the second reagent with thefirst reagent. In some embodiments, the method further comprisesinserting the grid into the apparatus following step (e). In someembodiments, step (f) is performed using a third reagent (e.g., adetectably labeled third reagent). In some embodiments, the thirdreagent is borne in a liquid.

In some embodiments, the first reagent is a cell (e.g., an adherentcell, a non-adherent cell, and a permeabilized cell. In someembodiments, the second reagent is an agonist (e.g., stimulator of thefirst reagent) or an antagonist (inhibitor of the first reagent).

In some embodiments, the first reagent is a binding agent. In someembodiments, the binding agent is a nucleic acid molecule (e.g., asingle-stranded nucleic acid molecule), an antibody, and a ligand.

In yet another aspect, the invention provides an apparatus comprising: aplate comprising a number of elements, said elements each having anidentical diameter and having a first surface energy, said elementsarranged in an array in an overlay having a second surface energy, and awall circumferential to the plate, wherein said overlay is a height overthe elements of between about 5% and 100% of the diameter of theelements.

In some embodiments, the first surface energy results in a hydrophilicsurface and the second surface energy results in a hydrophobic surface.In some embodiments, the height of the overlay over the elements isbetween about 10% and 80% of the diameter of the elements. In someembodiments, the height of the overlay over the elements is betweenabout 20% and 50% of the diameter of the elements

BRIEF DESCRIPTION OF THE DRAWINGS

Those skilled in the art should more fully appreciate advantages ofvarious embodiments of the invention from the following “DetailedDescription of the Invention,” discussed with reference to the drawingssummarized immediately below.

FIG. 1A is a schematic representation of an exploded view of anon-limiting system of the invention comprising an apparatus and aremovable grid;

FIG. 1B is a schematic representation of an assembled sectional view ofthe system depicted in FIG. 1A;

FIGS. 2A-2B are schematic representations showing exploded and assembledviews of a non-limiting system of the invention, wherein thenon-limiting removable grid depicted has large tabs for ease ofhandling;

FIG. 3A is a schematic representation of a non-limiting apparatus of theinvention having an elongate geometry;

FIG. 3B is a schematic representation of an exploded view of theapparatus of FIG. 3A with a non-limiting removable grid of theinvention;

FIG. 3C is a schematic representation of an assembled view of theapparatus of FIG. 3A and the grid of FIG. 3B;

FIG. 4A shows a non-limiting embodiment of the removable grid of theinvention where the removable grid has a reservoir connecting more thanone through-hole of the grid;

FIG. 4B shows the grid of FIG. 4A loaded with sample droplets;

FIG. 5 is a schematic representation of a non-limiting system of theinvention having an apparatus with a 1536-element plate configurationand a removable grid with 96 through-holes;

FIGS. 6A-6B are schematic representations showing exploded and assembledviews of another non-limiting system of the invention have a 96-wellmicroplate configuration;

FIGS. 7A-7B are schematic representations showing exploded and assembledviews of yet additional non-limiting system of the invention having a384-well microplate configuration;

FIG. 8A is a schematic representation showing a cutaway view of anon-limiting embodiment of the invention having an apparatus and anon-limiting grid comprising a lid with baffles;

FIG. 8B is a schematic representation showing an underside view of thelid of FIG. 9A;

FIG. 8C is a schematic representation showing a close-up sectional viewof a portion of the lid of FIGS. 8A-8B, showing baffles (i.e.,offsetting features) which create an air gap between the lid and thegrid;

FIG. 9 is a schematic representation showing an alternate non-limitinglid for airtight sealing;

FIG. 10A is a schematic representation showing a cutaway view of anon-limiting embodiment of the invention having an apparatus and anon-limiting grid comprising a lid with baffles and a hole forintroducing fluid (e.g., inert fluid);

FIG. 10B is a schematic representation showing a cutaway view of the lidof FIG. 10A showing the reservoir surrounding the hole;

FIG. 10C is a schematic representation an underside view of a lid ofFIG. 10A;

FIG. 10D is a schematic representation a close-up sectional view of aportion of the non-limiting lid of the invention depicted in FIGS.10A-10C, the grid having notches on the surface of the grid that touchesthe plate of the apparatus in the assembled system;

FIG. 11 is a schematic representation of a non-limiting apparatus of theinvention, where the hydrophobic overlay is raised a height of at least5% of the diameter of a hydrophilic element above the hydrophilicelements. In the lower panel of FIG. 11, a close-up view of across-section of the non-limiting apparatus is depicted.

FIG. 12 are a series of photographs of sp2 cells on a “recess”DropArray™ plate, incubated overnight followed by a series of washingstep performed by DropArray™ Accelerator LT100. The left panel shows awell with cells before washing after overnight incubation. The threepanels on the right show the same well after 1^(st), 2^(nd) and 6^(th)wash.

DETAILED DESCRIPTION OF THE INVENTION

The invention provides apparatuses and methods for performing multiplereactions in small volumes of liquid. The invention provides thehigh-throughput capabilities of protein microarrays with the specificityand robustness of microtiter-plate assays such as ELISAs and cellproliferation assays.

The further aspects, advantages, and embodiments of the invention aredescribed in more detail below. The patents, published applications, andscientific literature referred to herein establish the knowledge ofthose with skill in the art and are each hereby incorporated byreference in their entirety to the same extent as if each wasspecifically and individually indicated to be incorporated by reference.Any conflict between any reference cited herein and the specificteachings of this specification shall be resolved in favor of thelatter. Likewise, any conflict between an art-understood definition of aword or phrase and a definition of the word or phrase as specificallytaught in this specification shall be resolved in favor of the latter.As used herein, the following terms have the meanings indicated. As usedin this specification, the singular forms “a,” “an” and “the”specifically also encompass the plural forms of the terms to which theyrefer, unless the content clearly dictates otherwise. The term “about”is used herein to mean approximately, in the region of, roughly, oraround. When the term “about” is used in conjunction with a numericalrange, it modifies that range by extending the boundaries above andbelow the numerical values set forth. In general, the term “about” isused herein to modify a numerical value above and below the stated valueby a variance of 20%.

Technical and scientific terms used herein have the meaning commonlyunderstood by one of skill in the art to which the present inventionpertains, unless otherwise defined. Reference is made herein to variousmethodologies and materials known to those of skill in the art. Standardreference works setting forth the general principles of recombinant DNAtechnology, biochemistry, chemistry, and immunology include Ausubel etal., Current Protocols in Molecular Biology, Wiley InterScience, NewYork, N.Y., (2007, and updates up to and including 2011); Coligan etal., Current Protocols in Immunology, Wiley InterScience, New York,N.Y., (2007, and updates up to and including 2011); Harlow and Lane,Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press,New York (1998); Lo et al., Antibody Engineering: Methods and Protocols,Humana Press, 2003; Sambrook et al., Molecular Cloning: A LaboratoryManual, 2nd Ed., Cold Spring Harbor Laboratory Press, New York (1989);and Kaufman et al., Eds., Handbook of Molecular and Cellular Methods inBiology in Medicine, CRC Press, Boca Raton (1995).

Microtiter plates allow running multiple reactions within multipleisolated compartments separated by physical walls. Many types ofchemical, biochemical, and biological reactions and assays are performedon microtiter plates, particularly when multiple reactions are performedin high-throughput analyses. For example, during the generation of anantigen-specific monoclonal antibody (and antibody-secreting hybridomacell) in accordance with the method Kohler and Milstein (see, e.g.,Nature 256 (5517): 495-497, 1975), different individual clones of cellsare grown in wells of microtiter plates. Antibody-containing supernatanttaken from the wells are screening for their ability to bind to theantigen of interest, and the identified clone can then be expanded forlarge-scale production of the antigen-specific monoclonal antibody.

Similarly, small molecules are routinely screened in high-throughputcell-based reactions on microtiter plates to determine the candidatemolecule to be further analyzed and formulated as a potentialtherapeutic. On a molecular level, screening of a potential therapeutic(e.g., a biological for its ability to antagonize an antigen-specificantibody or a ligand-specific receptor) are routinely screened usingmicrotiter plates in assays such as ELISAs.

Many different types of microtiter plates are available commercially.However, while the presence of physical walls separating the differentwells of the microtiter plate helps to prevent cross-contamination, thewalls also hinder easy and convenient washing by flowing a bulksolution. Instead, an individual compartment needs to be washedone-by-one.

The apparatus described in PCT Patent Publication No. WO2008/06136 (alsopublished as US patent publication no. 20100285573; incorporated hereinby reference in its entirety) employs a virtual wall technology thatenables running multiple reactions without physical walls. In thisapparatus (a virtual wall plate and system is sold commercially underthe trademark DropArray™ by Curiox Biosystem Pte. Ltd. (Signapore) orits distributors (e.g., Acelearium Lab Solutions, Inc., Westford, Mass.,USA), instead of wells, hydrophilic elements are surrounded by ahydrophobic overlay. Liquids drops are thus held in place on theelements using surface energy effects. Such characteristics offer manyadvantages over standard microtiter plates including, for example, easyand convenient washing by flowing a washing solution across the surfaceof the apparatus.

It should be noted, however, a physical wall in a microliter plate doesprovide some benefits. For example, the presence of a physical wallbetween wells can expand the capacity of the volume that can be held ineach well. In one model of the DropArray™ plate, an element (or well) of2 mm diameter on the plate can hold a liquid up to 3 uL for typicalhandling. When the volume of a liquid increases beyond 3 uL, however,liquid can break off easily from the hydrophilic element. This is due toincreased inertia (kinetic energy applied to a drop) coming fromincreased height of the drop while the cohesion of a liquid and adhesionbetween a liquid and hydrophilic surface remain same. By increasing thevolume that each well (or element) can hold, each well could hold moresample, or have better detection of the sample or reaction product(e.g., where the detection reagent is borne in a liquid).

Another benefit provided by the presence of a physical compartmentseparated by a wall on a standard microtiter plate may be that the wallscan facilitate dispensing of a liquid into individual wells. Whendispensing onto a virtual wall plate (or another similar plate withshallow wells), where a well (also called an element) is defined bysurface tension, the dispensed liquid should be delivered onto thefeature relatively precisely onto the element. In contrast, when liquidis dispensed into a well separated by a physical wall, the dispenser candrop the liquid anywhere within a well.

The presence of physical walls may reduce the chance of spilling afluidic content contained in a DropArray™ plate or a similar plate withextremely shallow wells. For example, in the configuration of DropArray™technology, a plate contains an array of drops is immersed in inertfluid (e.g., the fluid sold under the trademark DropArray™ Rinsing Oil™sold by Curiox Biosystem). When such plate with fluidic content istransported, the movement of the plate creates momentum in the fluidiccontent inside of a plate, which leads to an unblocked wave of fluid,often resulting in spillage when such wave reaches the end of the plate.The physical wall of the grid functions as a barrier dampening theunblocked flow of fluid.

Additionally, compartmentalization by a physical wall on a standardmicrotiter prevents accidental cross-contamination by displacement of adrop. When a drop is placed onto a hydrophilic element of a DropArray™plate, the interaction between the drop and hydrophilic feature mostlyresult from hydrophilic-hydrophilic attraction, which is relativelyweak. Therefore, a drop can be displaced relatively easily by externalforce, such as shear force generated by the flow of inert fluid presentin the plate or physical shock applied from sudden movement of a plate.

Thus, for microtiter plates, there are benefits to having no physicalwalls (i.e., virtual walls), and benefits to having physical walls.Thus, it would be useful to have a virtual wall plate to which physicalwalls could be added or removed when desired. Thus, one aspect of thepresent invention thus stems from the development of a removable gridthat can be inserted onto a virtual wall plate when the presence ofphysical walls is desired (e.g., during loading of sample or duringincubation of the sample to allow a reaction to occur), and removed whenthe presence of physical walls is undesired (e.g., during washing of theplate). Surprisingly, the inventors discovered that when a grid made inaccordance with the invention is inserted onto the virtual wall plate, aseal is formed thereby preventing cross-contamination between the wellscreated by the grid's physical walls. Indeed, if volumes within the wellare small, if a drop on the hydrophilic element is displaced (e.g., ifthe plate is physically jarred), the drop is still contained within thearea enclosed by the physical walls of the grid, thereby eliminating thepossibility of cross-contamination into an adjacent well. Often suchdrop is attracted to a hydrophilic element again as the drop issurrounded by hydrophobic surfaces of the overlay, the inert fluid, andthe physical wall of a grid. Additionally, the physical wall of a gridfunctions as a barrier and reduces the flow of an inert fluid within theplate, thereby minimizing the chance of a drop being displaced.

Accordingly, in a first aspect, invention provides a system comprisingan apparatus and a removable grid insertable into apparatus. Theapparatus may comprise a plate comprising a number of elements having afirst surface energy arranged in an array within a thin overlay having asecond surface energy; and a wall circumferential to the plate. In someembodiments, the first surface energy results in a hydrophilic surfaceand the second surface results in a hydrophobic surface. The removablegrid insertable into the apparatus may be positioned over the plate andwithin the wall of the apparatus, where the grid comprises dividersenclosing a number of through-holes, the through-holes spaced in thegrid to allow alignment of the through-holes of the grid over theelements in the plate when said grid is inserted into the apparatus,wherein said dividers of the grid inserted into the apparatus form sidesof wells bottomed by the plate and at least one element on said plate.

In another aspect, the invention provides a removable grid insertableinto an apparatus comprising a plate comprising a number of elementshaving a first surface energy arranged in an array within a thin overlayhaving a second surface energy and a wall circumferential to the plate,said grid comprising dividers enclosing a number of through-holes, saidthrough-holes spaced in the grid to allow alignment of the through-holesof the grid over the elements in the plate when said grid is insertedinto the apparatus, wherein said dividers of the grid inserted into theapparatus form sides of wells bottomed by the overlay of the plate andat least one element on said plate.

In a non-limiting example of the system and grid of the invention, aflat plate (e.g., a virtual wall plate) can be patterned with elementscomprising molecules of interest to create an array. As describedherein, the elements are surrounded by hydrophobic coating. Thevirtually flat plate with a hydrophobic overlay and hydrophilic elementpattern within that overlay is similar to the surface characteristics ofa typical array.

In some embodiments, the dividers of the grid have a second surfaceenergy. In some embodiments, the second surface energy results in ahydrophobic surface.

In one non-limiting embodiment, a grid made of a hydrophobic plasticmaterial such as polypropylene (PP) or polytetrafluoroethylene (PTFE)can be placed on the flat substrate to create ‘removable’ wells. In someembodiments in using one of the grids or the systems disclosed herein,the grid is placed on the substrate only during incubation. In someembodiments, the grid is placed on the plate during the loading step.During a washing step (or at other convenient times), the grid isremoved from the plate in order to facilitate a whole plate washingwithout fluidic interruption from the presence of the grid.

One non-limiting example of a grid and system of the invention is shownin FIG. 1A, and FIG. 1B shows an assembled sectional view of the systemof FIG. 1A. As shown in the exploded view of the system in FIG. 1A, anapparatus 100 has a plate 110 surrounded by a wall 140. The plate 110has a plurality of elements 120 separated from each other by an overlay130. The elements 120 and overlay 130 have a surface energy differencesuch that the elements 120 can each attract a liquid. For example, theelements 120 may be hydrophilic and the overlay hydrophobic so thataqueous liquids can be adhered to the elements 120 without crosscontamination. The elements 120 may be transparent to aid in opticalobservation. The plate 100 may be used, for example, with the methodsdisclosed in PCT/SG2007/0003939, WO2008/063136, and WO2010/120249 (allof which are hereby incorporated by reference in their entirety). Notethat the walls or exterior structure 140 of the apparatus shown in FIG.1A allows for ease of manual or robotic handling and defines a reservoirabove the plate 110. The reservoir can be used to hold a washing fluid(one that is miscible with liquid held on the elements 120).

A removable grid 150 (shown above the apparatus in FIG. 1A) can beinserted into the walls 140 of the apparatus to partition the reservoircreated by the walls with dividers. The grid 150 shown in FIG. 1Aincludes a plurality of through-holes 160 that outlined by dividers 180,where the through-holes 160 have a spacing that corresponds to theelements of the plate 110. The grid 150 may fit snugly into the exteriorstructure (or wall) 140 so as to enforce positioning of thethrough-holes above the elements. The grid 150 may include handlingstructures 170. The handling structures 170 may be tabs that overhangthe ends of the grid 150. In some embodiments, such handling structure170 facilitates removal of the grid from the apparatus.

As shown by the interface between the plate 110 and the grid 150 in FIG.1B, wells are created which are bottomed by the plate and walled by thedividers of the grid. As shown in FIG. 2, the plate forming the bottomof each well comprises at least one element within the well. One or morereagents may be added to the through-holes 160 to increase the volume ofliquid that may be contacted with any given element 120 or to aid in theaddition of different reagents to different elements.

Both the grid and exterior structure (i.e. walls) of the apparatus ofthe system of the invention may be made by injection-molding plastics bywell known techniques. The plate of the apparatus may be, for example,made from glass patterned with a polytetrafluoroethylene (PTFE) material(e.g., the polytetrafluoroethylene (PTFE) sold under the trademarkTeflon® by DuPont) such that the elements are hydrophilic (e.g., fromthe hydrophilic glass) while the overlay is hydrophobic (e.g., from thehydrophobic PTFE). FIG. 1 shows an example of the removable grid placedon top of a virtual wall plate. Note that the non-limiting plate shownin FIG. 1 has SBS (Society for Biomolecular Screening) standard 384features (i.e., virtual wells or elements arranged in a 24×16 array).The non-limiting plate and apparatus of the invention depicted in FIG.1A has 2 mm diameter hydrophilic elements. The external dimension of agrid fits the internal dimension of the walls of the apparatus such thatwhen the grid can be inserted into apparatus (see FIG. 1B).

In the embodiment of the grid and system shown in FIGS. 1A and 1B, thepattern of the through-holes in the grid follows the pattern of theelements in the underlying plate exactly. In some embodiments, thedividers of the removable grid are, for example, 8.0-12.0 mm height.When the grid is inserted into the apparatus to create wells walled bydividers of the grid and bottomed by the plate comprising a singleelement, each well can hold liquid of up to 40-50 uL.

Note that although FIGS. 1A and 1B depict a DropArray™ virtual plate,other virtual wall plates similar to that shown in FIGS. 1A and 1B arecommercially available, for example from Erie Scientific (a division ofThermo Scientific) and from Cytonix Corporation (Beltsville, Md., USA;sold under the trademark u-Plates™). The grid of the invention may beused inserted into apparatuses containing such virtual wall plates tocreate wells dividers of the grid and bottomed by the plate comprisingat least one single element (i.e., single well with virtual walls).

It should be noted that one potential trouble in using a removable gridin the systems of the invention is cross-contamination between wellscreated walled by dividers of the grid and bottomed by the plate due toleaking of a fluid from one well to another well via a path under grid,as a grid is simply positioned on top of a bottom plate without sealing.The leakage of a liquid between wells can be controlled by adjusting thethickness of the walls and the surface tension of the grid. When thegrid either is made of, for example polytetrafluoroethylene (PTFE) orpolypropylene (PP), or is coated with such material on the surface, thesurface of the grid presents significantly hydrophobic characteristics.The hydrophobic surface prevents the wetting of the grid by the liquidof a drop contained in each well. In some embodiments, the thickness ofthe grid dividers may be in the range of about, for example, 0.5-3.0 mm,or may be in the range of about, for example, 0.5-1.5 mm in thickness.The thickness of the grid dividers may be adjusted depending numerousfactors including, without limitation, the physical characteristics ofthe liquid of a drop (e.g., how much reagent is borne by the liquid) andthe diameter of the element. The thickness of the grid may also dependupon the presence of an inert fluid on the plate.

Thus, in some embodiments of the invention, the apparatus of the systemfurther comprises an inert fluid that coats the plate with a thin layer.By “inert fluid” is meant a fluid that is immiscible with a hydrophilicliquid (e.g., water or a tissue culture media). Non-limiting examples ofinert fluids of the invention include the perfluorinated hydrocarbonliquid sold under the trademark Fluorinert™ name by the 3M Corporation(St. Paul, Minn., USA) and the immiscible fluid sold by CurioxBiosystems (Signapore) under the trademark Rinsing Oil™. The presence ofhydrophobic inert fluid can reduce the possibility of the leakagebetween neighboring wells in the presence of a hydrophilic liquid (e.g.,a liquid bearing a reagent). The hydrophobic inert fluid thus makes ahydrophobic surface of a solid substrate such as PP and PTFE moreresistant against wetting by a hydrophilic liquid.

In some embodiments, the inert fluid added to the plate of the apparatusafter the plate has been loaded with a liquid containing a firstreagent.

As used herein, by “reagent” is meant any molecule or vehicle (e.g.,liposome, a living eurkaryotic or prokaryotic cell, or a non-livingeukaryotic or prokaryotic cell) comprising at least one molecule. By“molecule” is meant any molecule including, without limitation,inorganic molecules and organic molecules (e.g., lipids, proteins,nucleic acid molecules, and carbohydrates).

In certain embodiments of the invention, the plate comprises a PTFEoverlay patterned onto a hydrophilic surface such that flat hydrophilicelements are exposed (the virtual wells) that are surrounded by the PTFEoverlay. In some embodiments, the diameter of each element is 2 mm, andeach element is separated horizontally or vertically from its adjacentelement by about 4.5 mm. In some embodiments, this results in a 384array from a 16×24 element array (see FIG. 1A). In a non-limitingapparatus of the invention, the plate is contained within a wall that isapproximately 8 mm in height. In some embodiments, the grid isconstructed of polypropylene (PP). In some embodiments, the grid is madeof polypropylene with 10-20% glass fillers in order to enhancemechanical strength of the material. Alternatively, the grid is made ofmetal, for example, such as aluminum, and coated with a hydrophobicresin, such as PTFE resin, in order to present a hydrophobic surface.

In some embodiments, the grid is made of metal or glass and coated withhydrophobic film (e.g., with PTFE or PP) in order to prevent it fromfloating on the inert fluid when inert fluid is added to the apparatus.Inert fluid has a high density. For example, the DropArray™ Rinsing Oilusually has a density of 1.5˜2 g/ml, much higher than a typical plasticmaterial such as polystyrene or polypropylene. Thus, it may be desirableto have the grid weigh more (e.g., be made of glass or metal) in orderto prevent flotation.

In some embodiments, the grid is designed to sit inside of the reservoirof the plate tightly. In some embodiments, each divider of a grid hasthickness of, for example, 0.5-2 mm with height of 5-10 mm. In someembodiments, each divider of the grid has a thickness of, for example,0.5-1.5 mm with height of 7.5 mm. In one non-limiting embodiment of theinvention, a grid may be optimized for the array format of a grid andthe design of a corresponding plate. When the grid is made of a plasticmaterial such as PTFE or PP, the grid can be produced by injectionmolding or a similar technique, which allows fabrication at reasonablylow cost while maintaining precision required. When a grid is made of ametal such as aluminum, it can be produced by a general machining methodavailable.

In another non-limiting embodiment of the grid and system disclosedherein, the grid further comprises handling structures that protrudeupward from the grid when the grid is inserted into the apparatus (seeFIGS. 2A and 2B). The handling structures (see FIGS. 1A-1B, and 2A-2B)provide a convenient grasp for user (e.g., a human or non-human user)grasp the grid and insert it or remove it from the apparatus of thesystem of the invention, as desired. Thus, in another embodiment of theinvention, the grid further comprises at least one structure on thesurface of the grid that does not touch the plate when the grid isinserted into the apparatus, said structure sized for a user to grab thegrid and insert or remove the grid from the apparatus.

Thus, the insertion and/or removal of a non-limiting grid of theinvention into or from an apparatus (e.g., a virtual wall plate such asCuriox Biosystem's DropArray™ plate) can be performed manually by ahuman user or automatically by an instrument. For example, an instrumentcan insert a grid into the apparatus by simply dropping the grid fromabove onto an apparatus such that the grid inserts into the walls of theapparatus and onto the plate of the apparatus. Then, the systemcontaining the grid inserted into the apparatus can move around in aliquid handling system for addition of reagents. In one embodiment, oncethe dispensing of the reagent and incubation are completed, the systemcontaining the grid inserted into the apparatus can be returned to theinstrument, where the grid can be removed from the apparatus by, forexample, picking up the grid (e.g., using the structure as describedabove) or flipping the entire plate upside down so that the grid willfall out of the apparatus under the influence of gravity. Once the gridis removed from the apparatus, the apparatus is ready for washing by abulk washing solution instead of well-by-well wash.

Thus, as described above, in some embodiments of the invention, theplate comprises 48 elements of 2 mm diameter, where each element isseparated by its horizontal and vertical neighbors by 4.5 mm. Aremovable grid fits snugly into the apparatus over the plate and withinthe walls. The apparatus may also have optional ramp structures allowingthe grid to sit, for example, 0.1-0.2 mm higher than the surface of theplate in order to allow inert fluid to escape through the gap betweenthe plate and grid upon dispensing of liquid into the through-hole ofthe grid. In this embodiment, the plate is coated with inert fluid bypouring inert fluid onto the plate and then draining the fluid off theapparatus. A coating of inert fluid will remain on the plate. The gridmay also be pre-soaked with the inert fluid in order to preventnon-specific and/or irreversible adsorption of a reagent in thethrough-hole. In some non-limiting embodiments, the grid may be made ofpolytetrafluoroethylene (PTFE) and is total 4 mm high while the bottom 2mm is the section with through-holes and the top 2 mm is the sectionwith large reservoir to hold the inert fluid. At both ends of the gridshown in FIGS. 2A and 2B, there are two protrusions of 2-4 mm high inorder to facilitate the handling of the grid in and out of theapparatus. In this non-limiting grid of the invention, 4-8 uL of areagent is dispensed into each though-hole.

FIGS. 3A-3C shows another non-limiting system of the invention. In FIGS.3A-3C, the apparatus 100 is elongate, in the general shape of amicroscope slide. In the non-limiting apparatus 100 shown in FIGS.3A-3C, the apparatus 100 further comprises one or more positioningstructures 300 for positioning a grid 150 such that the through-holes160 are aligned over the elements 120. FIG. 3C shows samples loaded intothe system of the invention.

Accordingly, in another embodiment of the invention, the apparatusfurther comprises a positioning structure adjacent to the interior ofthe wall so as to guide alignment of the through-holes of the grid overthe elements when the grid is inserted into the apparatus.

To facilitate the loading of the apparatus of the invention with areagent-carrying liquid, the through-holes of the grid may be joined ina larger reservoir, where the liquid may be added anywhere to thereservoir and allowed to flow into the through-holes to drop onto theelements of the underlying plate of the apparatus. FIGS. 4A and 4B showyet another non-limiting grid of the invention showing this reservoir.As shown in FIG. 4A, the dividers defining the through-holes are notrectangular but, rather, outline circular through-holes. A largerreservoir encompassing at least two through-holes facilitates additionof a reagent-bearing liquid to the underling plate when the grid isinserted into the apparatus (see FIG. 4B, where the droplet from thepipet-tip need not be exactly aligned with the through-hole in order toadd the liquid to the element).

Accordingly, in another embodiment of the disclosed grid and system, theinvention provides a grid further comprising a reservoir encompassing atleast one through-hole of the grid, said reservoir on the surface of thegrid that does not touch the plate when the grid is inserted into theapparatus.

A non-limiting embodiment of the grid disclosed herein can includefeatures to minimize evaporation. For example, if the through-hole issmall and holds less than 10 uL of a reagent, the reagent may experienceevaporation during incubation. The evaporation of the reagent can beminimized by either building bigger through-holes to hold a biggervolume of a reagent, say more than 10 uL. Alternatively, the grid mayhave a built-in reservoir above the top surface that is structured tohold inert fluid. For example, in FIGS. 3A-3C, the grid comprises areservoir that encompasses all the through-holes of the grid. In theembodiment shown in FIGS. 3A-3C, the reservoir is formed from an outerwall encompassing all the through holes and extending normal to theplane of the holes to a height sufficient to allow Rinsing Oil to coverliquid loaded in the holes. In FIGS. 4A-4B, numerous reservoirs, eachencompassing more than one through-hole of the grid, are shown. In theembodiment shown in FIGS. 4A-4B, the grid can be designed with a seriesof long reservoirs at the top, where the inert fluid can be dispensed,effectively sealing off the reagent in the through-holes in the similarmanner. Once the through-holes in the grid are filled with a reagent,inert fluid can be added into the reservoir, so that the reagents withinthe through-holes and/or on the elements of the plate are sealed by theinert fluid, thereby minimizing evaporation.

Of course, the skilled practitioner will realize that the through-holesneed not be circular when combined with this reservoir feature. Forexample, one can easily imagine the square through-holes shown in thegrid of FIG. 1 combined with the reservoir shown in FIGS. 4A-4B.Moreover, the reservoir may encompass all of the through-holes on thegrid (see the grid of FIGS. 3B and 3C). Moreover to aid in directing thefluid to the droplet, one can easily appreciate that the dividers of thegrid may also be funnel-shaped or sloped, such that a liquid dropletplace into the reservoir (if present as in FIG. 4A-4B or in FIGS. 3B and3C) or absent (as in FIG. 1) is directed to the element on theunderlying plate.

Indeed, the shape of the well formed by the dividers of the grid aswalls and bottomed by the plate may be readily changed for a betterperformance. For example, the physical shape of a grid divider may be ina rectangular shape. Alternatively, the shape may have a varyingthickness, where the bottom of the divider very thin and the wallthickness increases in the upper part. The shape of a grid divider maybe adjusted to fit the designed application best while considering theproduction cost. The shape of a grid divider with pointy bottom isexpected to decrease the convection of the inert fluid present while thegrid is being removed.

In some embodiments, the invention also provides for a grid and a systemwhere each through-hole of the grid itself encompasses an array ofelements on the plate when the grid is inserted into the apparatus ofthe invention. Microtiter plate analyses allow large numbers of probesor assays to query a given sample. However, users of an array (e.g., amicrotiter plate or a virtual wall plate such as the DropArray™ plate)may have multiple or numerous samples to analyze against a fewer numberof array elements than is present in a given array. This limitation issolved by yet another embodiment of the present invention.

Accordingly, in some embodiments, the invention also provides aremovable grid with a lower number of through-holes than the number ofelements on the plate of the apparatus into which the grid may beinserted. Thus, each through-hole of the grid is aligned over more thanone element in the plate of the apparatus. Thus, portions of the arrayedelements of the plate can be exposed to different samples introducedthrough the through-holes of the grid.

FIG. 5 shows a non-limiting example of this embodiment of a system ofthe invention. In FIG. 5, a removable grid with 96 through-holes is tobe inserted into apparatus with a 1536-element plate configuration.Thus, each through-hole in the grid encloses 16 elements when the gridis inserted into the apparatus. The grid may contain a second reagent ofa same kind or different kind as the reagent contained on the element ofthe plate, depending on the need. Thus, each of those 16 elements can beexposed to the same second reagent at the same time in a multiplereaction. In such configuration, the user can obtain up to 1536 datapoints with tools compatible with 96-well format, which can be easilyfound in a typical research laboratory.

This array within an array configuration of a grid and/or system of anon-limiting embodiment of the invention is useful for high through-putscreening. For example, it may be desirable to screen sixteen differenttypes of antibodies for their varying abilities to bind an antigen. Thesixteen antibodies can be patterned 96 times onto the 1536-element plateof the apparatus. Upon insertion of the grid into the apparatus, 96different potential antigens can be added through the through-holes ontothe apparatus. Because of the hydrophobic spaces between the elements(with or without coating of the hydrophobic overlay with an inertfluid), the potential antigen-containing liquid will pool onto theelements containing the antibodies. After removal of the grid, washingof the plate, and replacement of the grid, detection of binding of theantibody to the potential antigen can be determined using conventionaldetection methods. For example, binding can be detected incubating thesystem with a detectably labeled anti-antigen antibody and detectingbinding of the anti-antigen antibody.

As used herein, by “detectably labeled” is meant that a reagent islabeled with a detectable entity. For example, the reagent may beradioactively labeled (e.g., with 3H, 32P, 14C, or 35S), fluorescentlylabeled (e.g., with fluorescein or phycoerythrin), or labeled with aentity that is detectable upon addition of a detectable substrate (e.g.,labeled with horse-radish peroxidase).

Of course in using any of the grids or systems of the invention, thenumber of reagents can be adjusted and designed conveniently dependingon analysis needs. For example, the number of reagents can be determinedby the design of an array—the size of each element (or spot) for eachreagent and the pitch (i.e., distance between element (or spots). In theexample of using standard microtiter plate size as a plate (availablefrom Society of Biomolecular Sciences), the array can follow thestandard specification of a 1536 well microtiter plate (See FIG. 5).Each element of, for example, 1 mm diameter, is separated by itshorizontal and vertical adjacent elements by 2.25 mm.

As described above, a non-limiting embodiment of a removable grid of theinvention may facilitate the dispensing of a liquid-borne reagent ontoeach element of the plate of the apparatus. In some embodiments, aninert fluid (e.g., Rinsing Oil available from Curiox Biosystems) isadded into the plate and drained in order to wet the surface of theplate. Then, a removable grid is positioned inside the apparatus asshown in FIG. 1B. A reagent solution is added into each well walled bythe dividers of the inserted grid and bottomed by the plate by, forexample, pipetting. With the presence of a physical well created by thegrid, it may be easier to dispense a reagent. Further because of thephysical wall, even if the droplet is not placed precisely onto theelement, the wall will prevent the droplet from cross-contaminating thedroplet on an adjacent element. Due to the hydrophobicity of the overlayand the grid dividers, the droplet will be attracted to the hydrophilicelement and will remain there.

In addition to aiding in dispensing a liquid-borne reagent onto theelements of the plate of the apparatus, the disclosed grid of theinvention detection of a reaction result at the end of an assay process.For example, when an ELISA assay is run on a virtual wall plate (e.g.,the apparatus described herein or a DropArray™ plate), the last step ofthe ELISA process is detection of binding of the sample to the plate. Ofmany detection methods currently available, absorbance (e.g., using acolorimetric detectable label) and luminescence (e.g., using afluorescent detectable label) are popular. In these particular methods,the quality of detection such as sensitivity and signal-to-backgroundratio may be affected by the volume of the liquid-borne detectablylabeled reagent. FIGS. 6A-7B and 7A-7B show examples of a 96 well systemand a 384 well system, respectively, where a removable grid insertedinto an apparatus can produce physical wells for adding increased volumeof a detectably labeled reagent on top of a hydrophilic element. Inother words, the removable grid can help to increase the volume of adetectably labeled reagent per well beyond what is practical without thegrid.

In such case of volume-dependent detection, the ratio of the surfacearea of a hydrophilic element and the volume of a detecting reagent mayaffect the quality of the data. In other words, the simple increase ofthe volume of a detecting reagent may not generate enough signalincrease due to the limited surface area of a hydrophilic element, e.g.,due to the number of active protein available on the surface of ahydrophilic element. When such challenge occurs, the shape of a gridthrough-hole can be the shape of upside-down funnel. For example, thebottom of the grid through-hole may have the same diameter as that of ahydrophilic element. Then, there is a slope to reduce the diameter ofthe through-hole quickly, for example at 25-85 degree. After the slope,the diameter of the through-hole stays smaller than that of thehydrophilic element. At the detection of absorbance, the smallerdiameter of the through-hole may be either same as that of the detectinglight beam or up to 50% bigger.

In an alternate embodiment of the invention, the through-holes of thegrid may have a diameter that is the same as or not significantly largeror smaller than the diameter of the element of the apparatus. In thisembodiment, the grid can be pre-loaded with the reagent-bearing liquidprior to its insertion into the apparatus. In this embodiment, theliquid loaded into the grid should be able to stay within thethrough-hole (and not simply flow out due to gravity) if the size of thethrough-hole and surface tension of the inner surface are optimized toovercome the downward force of gravity. When the grid is inserted intothe apparatus, the liquid in the grid will be attracted to thehydrophilic element and will adhere to the element of the plate and notthe through-hole of the grid.

In some embodiments of the invention, the grid further comprisesoffsetting features on the surface of the grid that touches the platewhen the grid is inserted into the apparatus. These offsetting featuresallow the grid to sit upon the second surface energy overlay on thesurface of the plate of the apparatus, but without sealing firmly to theplate due to surface tension. The discovery of the applicability of suchoffsetting features was realized when the user had difficulty removingthe grid from the apparatus without dislodging or jarring the apparatussuch that the liquid droplets on the elements were dislodged. The sealbetween the grid and the second surface energy overlay on the surface ofthe plate of the apparatus can be altered depending upon whether theplate or the grid or both had been previously rinsed (and hence coated)with inert fluid. The offsetting features also allow the easy removal ofexcess inert fluid to be drained off the apparatus without having toremove the inserted grid.

Accordingly, in some embodiments, offsetting features are present on thesurface of the grid that touches the plate of the apparatus when thegrid is inserted into the apparatus. Interestingly, when such a gridwith offsetting features is inserted into the apparatus, the wellcreated which is walled by the dividers of the grid and bottomed by theplate may be as capable of holding liquid within the well as a gridwithout offsetting features. This is likely due to the shallowness ofthe offsetting features and/or the hydrophobic energies of the grid andthe overlay of the plate and, optionally, in the presence of inertfluid.

In further embodiments of the invention, the grid further comprises aplane perpendicular to the dividers of the grid attached to the surfaceof the grid that does not touch the plate when the grid is inserted intothe apparatus, wherein the plane covers all of the through-holes of thegrid. The plane (or lid) covers the entire apparatus when the grid isinserted into the apparatus. In some embodiments, the plane furthercomprises side planes perpendicular to said plane, said side planesparallel to and shorter than the dividers of the grid. In someembodiments, the grid further comprises offsetting features between thedividers and the plane.

A plate is often covered with a lid to protect a fluidic content inside.For example, a microtiter plate, which is popular in running multiplereactions in a given footprint, comes with a lid to prevent evaporationand protect the content inside from contamination by the surrounding. Atpresent, in most microtiter plates, fluidic content is contained in anarray of small compartments divided by physical walls, for example, in amanner of 24, 96, 384, and 1536 well format. The primary function of thephysical walls is to separate the fluidic content from each other inorder to prevent cross-contamination.

When a plate (such as the apparatus described herein) is designedwithout a physically dividing wall in a hollow pocket, e.g., a hollowreservoir with a flat slide at the bottom, a conventional lid leads toeasy spilling of a fluidic content. This is because there is no barrier(such as a physical wall) to dampen the generation of a wave produced byfluidic content within a plate. When the wave is formed duringtransportation, a relatively tall wave of the fluid collides with theside wall and lid and leads to the leakage of the content. Furthermore,waves of inert fluid inside may displace a drop from a hydrophilicfeature. The displaced drop can easily move around and merge with a dropon another hydrophilic feature, leading to cross-contamination.

In one embodiment of the present invention, a lid comes with a grid ofphysical walls attached to the flat, wide part of a lid in aperpendicular manner. In this non-limiting embodiment of the invention,the grid-attached a lid provides benefits similar to those of aremovable grid described earlier. The grid of physical walls functionsas a barrier against the flow of the fluidic content, particularly in ahollow plate, reducing the spilling of fluidic content by, for example,accidental shaking. In addition, an accidentally displaced drop will beconfined within a compartment created by the grid without thepossibility of merging with a neighboring drop. In fabrication of a lid,a wide, flat, often transparent area is preferably made of transparentpolystyrene, polycarbonate or similar material for optical clarity. Agrid attached to the flat area is preferably made of hydrophobicpolypropylene (PP), polytetrafluoroethylene (PTFE) or similarlyhydrophobic material. Although the grid is described here as attached,the grid-attached lid can be a monolithic structure, or multiplestructures adhered or welded together, depending on the manufacturingstrategy, several or which are well-known in the art.

In some embodiments of the invention, the lid attached to the removablegrid is simply a typical lid that is attached to all (or most) of thesurfaces the dividers of the grid that do not contact the apparatus whenthe grid is inserted into the apparatus. In some embodiments, the lid(with attached grid) simply sits on the apparatus by gravity, where theinner surface of the lid touches all (or most) of the top of the wallsof the apparatus.

It should be noted that depending on specific intended application, insome embodiments, a lid of the invention may come with additionalfeatures. For example, a lid may come with a gasket and littleprotrusions to grab in order to provide water-tight or nearlywater-tight sealing against a plate when assembled. In an example ofautomation, it should be easy and simple to place or remove a lid in andout of a plate in a simple automation process, for example, by a roboticarm. In an application for cell-based assays, often the plate assembledwith a lid is required to allow sufficient air exchange between theexternal and internal ambience and between different compartments withina plate. In such application, it is important that a lid is built withdesigns and features that ensure necessary air exchange occurring.

The physical walls (i.e., dividers of the grid) that are attached to theflat, wide area of a lid may come with a range of format, 24, 96, 384,and 1536. The thickness of the dividers can range, for example, from 0.5mm to 3 mm, depending on the format and the size of hydrophilic elementsof the plate. FIGS. 8A-8C show a non-limiting example of a lid for theformat of a 96-well microarray. FIG. 8A shows a cutaway view of the lid.In this non-limiting embodiment, the dividers of the grid are attachedto the lid through small contact points such as projected columns. FIG.8B shows the lid of FIG. 8A upside down, and FIG. 8C shows across-sectional view of the lid of FIG. 8A showing offsetting features(e.g., baffles) that create an air gap between the flat part and gridpart.

In one embodiment of fabrication, a grid may be made of PP, preferablywith 10-20% glass fillers for PP, in order to enhance mechanicalstrength of the material, or PTFE for its superior hydrophobicity.Alternatively, a grid is made of a metal, for example, such as aluminum,and coated with a hydrophobic resin, such as PTFE resin, in order topresent a hydrophobic surface. In some embodiments, a grid may bedesigned to sit inside of the reservoir of the plate tightly. The wallof a grid has thickness of, for example, 0.5-3 mm, with a height of 5-10mm, optimized for the array format of a grid and the design of acorresponding apparatus. In some embodiments, when a grid is made of aplastic material such as PTFE or PP, the grid can be produced byinjection molding or a similar technique, which allows fabrication atreasonably low cost while maintaining required precision. In someembodiments, when a grid is made of aluminum, it can be produced bygeneral machining method available. The fabricated grid is then attachedto a flat lid part by various adhesion methods such as gluing,ultrasonic bonding, etc. In some embodiments, a lid part may be made ofa transparent or non-transparent material such as glass, metal, and awide range of plastic materials. In some embodiments, a lid part may bemade of a transparent plastic material such as polystyrene,polycarbonate, or cyclic olefin copolymer. The lid part can also beproduced by injection molding or a similar technique, which allowsfabrication at reasonably low cost while maintaining precision required.

In another embodiment, the contact point between the barrier and theflat, wide area of a lid may be not completely sealed. For example, thecontact of the flat part and grid can be made through small columnarspacers when airflow in and out of the assembled plate is necessary foran intended application; for example, working with aerobic cellcultures. These air gaps facilitate the airflow between differentcompartments and external ambience in a similar manner to what wouldhappen in a conventional microtiter plate during a similar application.As a result, cell-based assays may be performed without stressing orkilling the cells or skewing the results due to differential aeration ofdifferent features.

Alternatively, when the lid is used for an application such as ELISA,where the airflow is not required, such air gap between the flat partand grid of a lid is unnecessary. Accordingly, in some embodiments, thegrid part may directly contact the flat part without any air gap betweenthem.

In addition, in some embodiments when the grid with attached lid isassembled with the apparatus, the grid divider may extend far enough(i.e., have enough height) to contact the plate or be in close proximityto the plate, for example less than 2 mm apart. However, if the distancebetween the end of the grid divider and the plate is too big, twopotential problems may arise: 1) flow of inert fluid under the griddivider on the surface of the plate is not reduced enough to minimizethe associated problems such as spill of fluid and displacement of dropsby the resulting shear force and 2) accidentally displaced drops maymove from its original compartment to a neighboring compartment in thegap between the grid divider and the surface of the plate leading tocross-contamination.

Thus, in some embodiments, air exchange is not desirable at all, and itmay be desirable to keep a plate covered with a lid air-tight andleak-free or a lid simply without any physical spacers. Thus in anotherembodiment, the invention provides an apparatus covered with agrid-attached lid, where the lids is air-tight and leak-free on theapparatus. FIG. 9 shows an embodiment of an air-tight, leak-free gridand lid of the invention. As shown in FIG. 9, the air-tight lid comeswith two catches on both long sides to snap fit to apparatus and rubberseal on bottom side of lid to create tight fit. Basically, the tight fitfeature will block the fluid spillage and minimize the evaporation offluid in the plate. At the same time, the lid can be still designed tobe stackable. To aid in showing the rubber seal and the catches to snaponto the apparatus, the grid attached to the lid is not shown in FIG. 9.

In yet another embodiment, a grid of the invention with a lid attachedmay be configured to accept an inert fluid into the apparatus while thelid remains assembled with the apparatus. FIGS. 10A-10D show a lidmodified from the version described above and depicted in FIGS. 8A-8C.As with the previously described grid with a lid, FIG. 8A shows the lidwith a flat part with an attached grid. As with the previously describedgrid with attached lid, the grid can have optional small, protrudingcolumns that ensure a gap between the lid and the grid for facilitatingairflow (see FIG. 10B). The lid-grid structure can also have offsettingfeatures (e.g., tabs or baffles) that offset the lid from the plate tocreate an air-flow gap (see FIG. 10D). Alternatively, the tabs can be onthe wall of the apparatus.

The grid with attached lid shown in FIGS. 10A-10D has three notablemodifications from the grid with attached lid shown in FIGS. 8A-8C.First, at one side of the lid, there is a small through-hole of 1-3 mm,where inert fluid may be added by, for example, a pipette. Thethrough-hole can be seen in the FIG. 10A, toward the right side. Second,right below the through-hole, there is a long, narrow chamber betweenthe sidewall of the plate and the first divider of the grid (as shown inFIG. 10B). Upon the addition of inert fluid (e.g. a perfluorocarbonDropArray™ Rinsing Oil as mentioned above), the fluid is firsttransferred to this chamber before spreading out through the entireplate. This chamber functions to lower resistance to added the fluid.Third, at the bottom of the grid walls, there are small notch-likeopenings of, for example, semicircular shape of 0.5 mm-3 mm diameter.The notches allow for fluid communication between “wells” of the platewhen the grid with attached lid is inserted into the apparatus. When thefluid is added through the small through-hole, it may spread throughoutthe entire plate by passing through the semicircular opening and/or gapbetween the end of the grid and the flat slide of a plate if there isany gap between the grid and the flat slide. However, the notches can besmall enough so as to retain the anti-wave features of the lid. It isnotable that a semicircular notche is present at the end of the dividerof a grid in both x- and y-direction.

The addition of the fluid while the lid is assembled with the plateprovides a few advantages. First, the potential displacement of adhereddrops by the flow of the fluid is minimized, as the flow of the liquidthrough the small gaps is designed to be gentle. Second, a displaceddrop, which could happen by any physical shock or sudden movement, willbe confined within the original compartment, preventingcross-contamination.

In a further aspect, the invention provides a method for performingmultiple reactions in parallel, the method comprising (a) providing asystem comprising (i) an apparatus comprising a plate comprising anumber of elements having a first surface energy arranged in an arraywith an overlay having a second surface energy and a wallcircumferential to the plate and (ii) a removable grid insertable intothe apparatus to be positioned over the plate and within the wall of theapparatus, said grid comprising dividers enclosing a number ofthrough-holes, said through-holes spaced in the grid to allow alignmentof the through-holes of the grid over the elements in the plate whensaid grid is inserted into the apparatus, wherein said dividers of saidinserted grid form wells bottomed by the plate and at least one elementon said plate; (b) adding a first reagent-containing liquid through thethrough-holes of the grid of the system under conditions where the firstreagent in the liquid adheres to the elements on the plate;

(c) adding rinsing oil to said plate in an amount necessary to coversaid plate; (d) draining excess rinsing oil from the plate resultingfrom step (c); (e) adding a liquid through the through-holes of the gridof the system, said liquid containing a second reagent suspected ofreacting with the first reagent; (f) removing the grid from theapparatus; (g) washing the apparatus; and (h) detecting reaction of thesecond reagent with the first reagent. In some embodiments, the methodincludes inserting the grid into the apparatus between steps (g) and(h). In some embodiments, step (h) is performed using a third reagent.In some embodiments, the third reagent is detectably labeled.

In a further aspect, the invention provides a method for performingmultiple reactions in parallel, the method comprising (a) providing asystem comprising (i) an apparatus comprising a plate comprising anumber of elements having a first surface energy arranged in an arraywith an overlay having a second surface energy and a wallcircumferential to the plate and (ii) a removable grid insertable intothe apparatus to be positioned over the plate and within the wall of theapparatus, said grid comprising dividers enclosing a number ofthrough-holes, said through-holes spaced in the grid to allow alignmentof the through-holes of the grid over the elements in the plate whensaid grid is inserted into the apparatus, wherein said dividers of saidinserted grid form wells bottomed by the plate and at least one elementon said plate; (b) adding a first reagent-containing liquid through thethrough-holes of the grid of the system under conditions where the firstreagent in the liquid adheres to the elements on the plate;

(c) adding a liquid through the through-holes of the grid of the system,said liquid containing a second reagent suspected of reacting with thefirst reagent; (d) removing the grid from the apparatus; (e) washing theapparatus; and (f) detecting reaction of the second reagent with thefirst reagent. In some embodiments, the method includes inserting thegrid into the apparatus between steps (e) and (f). In some embodiments,step (f) is performed using a third reagent. In some embodiments, thethird reagent is detectably labeled.

In some embodiments, the first reagent is a cell (e.g., an adherentcell, a non-adherent cell, and a permeabilized cell). In someembodiments, the second reagent is an agonist or antagonist.

In some embodiments, the first reagent is a binding agent. By “bindingagent” is meant a molecule that can bind with specificity to anothermolecule (including, for example, a molecule on a cell). Thus bindingagents include, without limitation, nucleic acid molecules (which canbind by hybridizing to nucleic acids with complementary sequences),antibodies (which can specifically bind to their antigen), receptors(which can specifically bind to their ligand or partner receptor),ligands (which can specifically bind to their receptors), specific tags(e.g., his-tags which specifically bind to nickel ion-containingmolecules), and individual member of a binding pair (e.g., streptavidinand biotin will specifically bind one another).

In using the various apparatuses and grids described herein, theinventors surprisingly discovered that non-adherent (i.e., suspensioncells) were retained on the apparatus without the grid when the heightof the overlay over the elements on the plate was at least 5% of thediameter of the elements. As described below in Example II and IV, thisdiscovery facilitates the use of the various embodiments of theinvention with reactions using suspension cells.

Accordingly, in still a further aspect, the invention provides anapparatus comprising a plate comprising a number of elements, saidelements each having an identical diameter and said elements having afirst surface energy, where the elements arranged in an array in anoverlay having a second surface energy, and a wall circumferential tothe plate, wherein said overlay is a height over the elements of betweenabout 5% and 100% of the diameter of the elements.

This aspect of the invention stems from the discovery that whensuspension cells are “plated” into the apparatus (with or without theaid of a grid inserted into as described herein), the suspension cellscan be retained in the apparatus if the overlay has a height above theelements of at least 5% of the diameter of the elements. For example, ina standard 384 element array, each element has a diameter of 2 mm. Thus,the height of the overlay in this aspect of the invention is at least0.1 mm over the elements.

Of course this height can vary. For example, in some embodiments, theheight of the overlay over the elements is between about 10%-80% of thediameter of the elements (e.g., for a 2 mm diameter element, the heightof the overlay is between about 0.2 mm and 1.6 mm). In some embodiments,the height of the overlay over the elements is between about 20% and 50%of the diameter of the elements (e.g., for a 2 mm diameter element, theheight of the overlay is between about 0.4 mm and 1 mm).

As described below, having an apparatus with an overlay height over theelements of at least 5% of the diameter of the elements is useful forretaining suspension cells on the apparatus during washing (e.g., wherethe elements are tissue culture treated).

In various embodiments of all aspect of the invention, the elements ofthe apparatus may be tissue culture treated. Thus, the flat apparatusand/or the apparatus comprising an overlay with a high over the surfaceof the elements of at least 5% of the diameter of such elementsdescribed herein may have tissue culture treated elements.

Methods to tissue culture treat surfaces are well known and include,without limitation, exposure of the surface to a vacuum-gas plasmatissue culture treatment process and exposure of the surface to coronadischarge. These processes generate highly energetic oxygen ions whichgraft onto the surface (e.g., where the elements of the plate are madeof polystyrene, the highly energetic oxygen ions graft onto polystyrenechains) so that the surface becomes hydrophilic and negatively chargedwhen tissue culture media or water is added (see, e.g., Hudis, M. PlasmaTreatment of Solid Materials. In: Hollahan, J. R.; Bell, A. T.; Ed.Techniques and Applications of Plasma Chemistry. John Wiley and Sons,New York; 113-147, 1974; Adaption of Plastic Surfaces for Tissue Cultureby Glow Discharge. J. Clinical Microbiology 2: 46-54; 1975. Andrade, J.D., Ed. Surface and interfacial Aspects of Biomedical Polymers. Vol. 2,New York, Plenum Press 1985; and Ramsey et al., Surface Treatments andCell Attachment, In Vitro, Vol. 20: 802-808; 1984). The more oxygen thatis incorporated on to the surface the more hydrophilic it becomes andthe better it is for cell attachment and spreading.

The following examples are provided to illustrate, but not to limit, theinvention.

Example I

As an example, one of the grids described above can be used in running acell-based assay, for example, ERK MAPK activation assay available fromthe Cellomics High Contect Screening division of Thermo Scientific(Product No. K0100071). Below is a standard protocol available from thesupplier (i.e., Thermo Scientific) for running the assay at 96-wellmicroplate.

When the assay is adapted to a virtual wall plate of 384-feature formatthe volume of the assay needs to be reduced accordingly. For example, ifa DropArray™ 384-well Cell Plate (commercially available from CurioxBiosystems) is employed, the “well” has only a 2 mm diameter glass areafor each element. With the help of a removable grid (such as one of theremovable grids described above), the process of miniaturization can besimplified.

The key challenge in miniaturization of this assay is the step of addinga stimulating compound such as Phorbol 12-myristate-13-acetate (PMA)into each element containing cells. For example, a 96-well microplatehas a cell solution volume of 100 uL. Then, 25 uL of PMA solution isadded on top of the existing 100 uL cell solution. In a 384-featurevirtual wall plate of 2 mm diameter feature, this means that the cellsolution is at the volume of 3 uL and added with another 0.75 uL,leading to the total volume of 3.75 uL. The total volume of 3.75 uL isover the range of the suggested maximum volume, 3 uL, for 2 mm diameterelement on the DropArray™ 384-well Cell Plate.

In a preferred example, the assay can be run in the following mannerwith the help of a removable grid. A standard 384-element virtual wallplate (e.g., a DropArray™ plate from Curiox Biosystems) with 2 mmdiameter element is prepared. An inert fluid, namely PerfluorocarbonRinsing Oil (commercially available from Curiox Biosystems), is added tothe plate followed by draining and leaving about 1 mL of Rinsing Oil inthe plate. Then a removable grid wet with the Oil is placed in theplate. In this example, the removable grid is made of PTFE and designedwith 2 mm diameter through-holes, 2 mm in height, with an additionalperipheral wall around the entire block of 6 mm height. The grid mayhave bottom-oriented offsetting features. For example, the removablegrid may have multiple 0.1 mm-0.5 mm high steps around the edge at thebottom, providing a little space between the virtual wall plate and themain frame of the grid. Such steps may facilitate the addition of areagent into a well, as the pre-existing inert fluid such as Rinsing Oilcan escape through the gap between the plate and the grid. Thehydrophobic surface of the grid and the plate prevents hydrophilicreagent, from leaking through the gap under optimal dispensingconditions. When the plate and removable grid is in place, the cellsolution is dispensed into the through-holes of the grid. The volume ofthe cell solution and compound solution such as PMA solution is reducedat the exact ratio of 25 times, for example, from 100 uL to 4 uL.

The volume of the cell solution dispensed to the virtual wall plate andgrid is 4 uL. Upon completion of the dispensing 10 mL of Rinsing Oil isadded into the plate for overnight incubation. On the next day, afterdraining the oil from the plate, leaving only a thin layer of Oil left,1 uL of PMA solution (25% volume with respect to the cell solution) isadded, leading to a total volume of 5 uL. Then, 10 mL of Rinsing Oil isadded for another 3 hour incubation. When the incubation is completed,the removable grid is removed from the plate, and the plate undergoes awhole plate washing process, for example, a wash by DropArray™Accelerator HT200. Then, the rest of the process is performed bystandard DropArray™ process using 3 uL of reagent at each step withoutthe need of a removable grid.

Cell Preparation Information

This protocol is optimized for NIH 3T3 cells (American Type CultureCollection, Product No. CRL-1658).

Briefly, NIH 3T3 cells are cultured using DMEM complete media (HyClone)supplemented with 10% fetal calf serum, 100 units/ml penicillin and 100μg/ml streptomycin. The cells are split when they reach 70-80%confluency (every 3-4 days) at a dilution of 1:3 to 1:5.

For an ERK activation study using a standard 96 well plate with physicalwalls, the cells are harvested with trypsin-versene mixture(BioWhittaker, Product No. 17-161F), diluted into DMEM Complete Medium,and cell density is determined (e.g., using a haemocytometer or othercell counter). The cell density is adjusted to 5×10⁴ cells/ml in DMEMComplete Medium and 100 μl of the cell suspension is added to eachvirtual well of an apparatus described herein having 96 wells (i.e.,approximately 5,000 cells/well. The apparatus containing the cells isincubated for 18-24 hours at 37° C. in 5% CO2.

It should be noted that for a standard 96 well plate, 100 μl per wellvolume is used unless indicated otherwise. This protocol requires ˜3hours to perform once compound incubation has been completed.

For this assay, PMA is prepared at a concentration of 500 ng/ml intoculture medium. Add 25 μl/well and mix thoroughly. Incubate 30 minutesat 37° C. For an agonist screen, the compound suspected of being anagonist replaces the stimulator (i.e., PMA is the stimulator). For anantagonist screen, add the compound suspected of being an antagonistbefore adding the stimulator.

Next, culture medium is aspirated and 100 μl pre-warmed FixationSolution (e.g., 4% formaldehyde in phosphate buffered saline (PBS)prewarmed to room temperature) is added to each well. The plate isincubated in a fume hood at room temperature for 10 minutes. Note thatpre-warming the Fixative Solution prior to adding it t the cells iscritical to maintaining cell integrity.

Next, the Fixation Solution is aspirated and the plate is washed oncewith 100 μl of 1× Blocking Buffer (e.g. 10% bovine serum albumin (BSA)in PBS). Next, the Blocking Buffer is aspirated and 100 μl of 1×Permeabilization Buffer (e.g., 0.1% Triton X-100 in PBS) is added. Theplate is then incubated for 15 minutes at room temperature.

Next, the Permeabilization Buffer is aspirated and the plate is washedonce with 100 μl of 1× Blocking Buffer. After aspirating the blockingbuffer, 50 μl of a Primary Antibody Solution is added per well. Theplate is then incubated for 1 hour at room temperature.

Next the Primary Antibody Solution is aspirated, and the plate is washedtwice with 100 μl of 1× Blocking Buffer and aspirated from the plate.Next, 50 μl of a Secondary Antibody Solution is added to each well. Theplate is then incubated at room temperature for 1 hour protected fromlight. The Secondary Antibody Solution is then aspirated, and the platedwashed twice with 100 μl of 1× Blocking Buffer. After aspirating, 200 μlof 1× Wash Buffer is added to each well. Next, the plate is sealed andevaluated on (e.g., on an ArrayScan HCS Reader). The sealed plates canbe stored in the dark at 4° C.

In accordance with the invention, the following is an example of runningthe ELISA test described above using the grid and system of theinvention. A Teflon-printed plate is prepared with a pattern of exposinga bare substrate surface of 1 mmdiameter with a distance of 2.25 mm ofTeflon-plating (e.g., forming a hydrophobic surface) between the bare(e.g., hydrophilic) elements. The surface of a Teflon-printed plate iscovered with ˜2 mL of Rinsing Oil (available from Curiox Biosystems) anddrained to leave a thin layer of the oil. A removable grid is added tothe plate, the grid can be made of either aluminum or polypropylene. Thegrid has 96 separated compartments with a wall of 0.5-1 mm thickness andcan fit inside the plate exactly (e.g., a snug or friction fit). If madeof aluminum, it can be coated with hydrophobic polytetrafluoroethylene(PTFE)-like material. Subsequently, a coating antibody solution of˜0.3-0.4 mL is added to each compartment. When the incubation iscompleted, the grid is removed from the plate, and the plate undergoes awhole-plate washing, where the plate is exposed to a bulk washingbuffer, a typically PBS buffer containing 0.05% Tween™ 20, and shakenfor a short duration of time. The same procedure of addition anddraining of the oil, placement of the grid, addition of a reagentsolution, and removal of the grid followed by washing can be repeated asmany as necessary. At the step of adding a fluorogenic substrate, thewashing is performed as usual by a whole plate method. Then, a solutionof a fluorogenic substrate of ˜30-40 mL is added as a bulk and quicklydrained by pouring out at, for example, 5-30 degree slanted. Thesolution left in the plate at such tilting is removed by manualpipetting. Upon complete removal of the substrate solution, the plate isleft with an array of small drops of the substrate solution at thevolume of 0.2-0.5 mL. Rinsing Oil (Curiox Biosystems) is quickly addedto the plate and the plate is read by a plate reader or scanner. Such aprocedure can be applied to a plate with 384-feature pattern on thesurface. In the example of the 384-feature plate, one compartment of96-well format grid will encompass 4 elements, for example of 2 mmdiameter and 4.5 mm pitch (i.e., a distance of 4.5 mm betweenhorizontally or vertically adjacent elements). Thus, if desired, asample held in the grid can be probed with 4 different capture probesimmobilized on the plate features.

In dispensing reagents into the compartments in the grid, the dispensingstep can be performed before or after placing the grid. If thedispensing is performed before the placement, then the wells of a gridshould be small enough to hold the reagents by capillary action, forgiven surface energies of a filling fluid and the grid. For example, thegrid with a compartment of bigger than 3 mm, it would generally bebetter to add reagents after the grid is placed on top of a plate. Whenthe compartment is smaller than 3 mm, the addition of the reagents cangenerally be performed before the grid is placed on top of a plate.

In order to facilitate the fluidics and assays, it may be desirable totreat the inner surface of a well of a grid to present a surface of aparticular nature. For example, the surface may be hydrophilic when itis desirable to better hold aqueous reagent in the well. In anotherexample, the surface may expose a non-fouling surface in order tominimize the non-specific adsorption of proteins to the surface duringincubation of reagents.

In particular, a hydrophilic surface may facilitate the addition offluid, usually aqueous solution, into the through-holes of a grid assuch surface will naturally ‘wick’ aqueous solution.

A grid for array-in-array applications can be added and removed freelyto a plate made with flat bottom slide. When the plate needs to bewashed, the grid can be conveniently removed from the plate. Then, theplate is washed by a bulk washing method instead of well-by-well washingmethod.

Example II

Suspension cells (e.g., suspension cell lines or blood cells) by natureare designed to stay in suspension and exhibit little adherence to aphysical substrate in contrast to adherent cells that show relativelystronger adhesion to a physical substrate. Due to the non-adherentnature of suspension cells, it is challenging to wash the cells, a stepthat is typically required for common and popular methods of studyingand such analyzing cells. During a washing process, the existing fluidicreagent containing cells is replaced with another fluidic reagent. Insuch process, cells are often exposed to a neutral fluidic reagentmultiple times by undergoing the step of addition, centrifuging anddecanting, before the addition of another fluidic reagent. The reasonfor washing with the neutral fluidic reagent is to ensure the completeremoval of the existing fluidic reagent before the addition of anotherfluidic reagent. Unlike handling of adherent cells, which stay adherentto a physical substrate and facilitate the removal of an existingfluidic reagent co-present with cells without loss of cells, suspensioncells can be easily lost during the washing process.

In the current practices, suspension cells usually undergo centrifugingbefore decanting of a co-present fluidic reagent. Centrifuging helps thecells to clump together and reduces the loss of cells during decanting.The requirement of centrifuging at every step of decanting makes thewhole process of cell analysis extremely tedious, laborious, andautomation-unfriendly. Furthermore, even after the centrifuge step, theclumped cells are still labile and easily come off during the liquidhandling step.

A simple modification of a DropArray™ plate or a similar flat plate withor without extremely shallow wells can enable the handling of suspensioncells in the same manner as that of adherent cells. A DropArray™ platecarries a flat slide at the bottom with hydrophobic and hydrophilicpattern, where hydrophilic features are employed in the similar capacityof a well in a conventional microtiter plate. For the intendedapplication with suspension cells, if the cells are laid as a singlelayer, the flat slide of a DropArray™ plate or a similar flat plate maybe employed to run a washing process in the same manner as for adherentcells. However, when the cells are laid as multiple layers on thesurface of a plate, the flat slide of a DropArray™ plate or a similarplate may be modified to introduce a little step at the contact betweenhydrophobic and hydrophilic area (i.e., create a “well” sided by thehydrophilic or hydrophobic through-holes and bottomed by the hydrophilicelement). Specifically, the hydrophilic elements are located slightlybelow the plane of overlay surface.

FIG. 11 shows an example of a flat plate to be assembled as an apparatus(e.g., a modification of a DropArray™ plate) for the application ofsuspension cell assay as a single layer. In the plate, the hydrophilicelements slightly recessed from the hydrophobic overlay of the slide.The degree of recess may vary depending on the diameter of hydrophilicfeature and stringency of washing required. For example, the recessionof 0.1-2 mm may be desirable for the diameter of 2 mm of hydrophilicfeature. The sidewall of the hydrophobic overlay (i.e., the exposedhydrophobic region inside the recess) may, in some embodiments, presentthe same hydrophobic surface at the surface of the hydrophobic overlay(i.e., the surface that will touch the bottom of the grid when the gridis inserted), but this is not always required. In the fabrication of aplate, for example, a transparent slide is made of a glass ortransparent polymeric material such as cyclic olefin copolymer (COC),polystyrene or polycarbonate. The hydrophobic overlay material may bemade of polytetrafluoroethylene (PTFE). The hydrophobic material can beeither attached to the transparent slide by non-cytotoxic adhesive orembedded by a process such as insert molding. When the hydrophobicmaterial is attached, the side of the hydrophobic material should betreated in a way that a glue or adhesive can bind, as PTFE or similarlyhydrophobic material generally shows poor adhesion. As for the depth ofthe recess and the diameter of a hydrophilic element, the depth of therecess is expected to increase as the diameter of the hydrophilicelement increases. The surface of a hydrophilic element may be treatedby, for example, gas plasma, or coated with a film such as a proteinand/or polypeptides such as fibronectin or polylysine in order toimprove the adhesion of the cells onto the surface of the hydrophilicelement.

The presence of the recess around hydrophilic features is believed toreduce the shear force from the fluidic movement of a washing solutioncreated from the shaking of a plate and impacting the cells sitting onthe surface of hydrophilic features. In the process of the presentembodiment, a plate is assembled with a cover to create a water-tightreservoir. Then, a washing solution is added into the reservoir followedby shaking or other means to create the flow of the washing solution.The flow of the solution helps to dilute reagents present on eachhydrophilic feature, which later is decanted from the reservoir.

It is desirable to fabricate the plate in a way that the flat slide ofthe plate presents both hydrophilic and hydrophobic surfaces on the sameplane. Such configuration maximizes the mixing of the reagent with awashing solution. However, the materials such as proteins and cellspresent on the hydrophilic surfaces experience relatively significantshear force by the movement of the fluid. For proteins in ELISA testsand adherent cells in adherent-cell-based assays, the washing conditionis optimized in a way that the direct shear force does not damage theoutcome.

When a flat slide of a plate is built with a slight recess, the shearforce applied on those materials on hydrophilic surface is substantiallyreduced while the mixing of the reagent in hydrophilic feature with awashing solution is reasonably satisfactory although the degree ofmixing is not as strong as that of a flat plate. Accordingly, theembodiment of the present invention features a recess depth that issufficient small to allow washing of the features yet sufficiently largeto discourage displacement of suspension cells.

FIG. 11 shows an example of an apparatus of the invention (i.e., flatslide patterned with hydrophobic and hydrophilic area and a surroundingwall), where hydrophilic area is slightly recessed from the plane ofhydrophobic area.

The configuration of DropArray™ plate exposing slightly recessedhydrophilic features was successfully tested and demonstrated minimalloss of suspension cells upon extensive washing of the plate. FIG. 12shows an example of washing test performed with a suspension cell line,sp2 cell line. In this test, sp2 cells were dispensed onto a 48-wellDropArray™ plate in a volume of 3 uL per well. The DropArray™ plate wascoated with Poly-L-Lysine to enhance the binding of the cells onto thehydrophilic surface. After overnight incubation at 37° C., the plateunderwent typical cell washing process in DropArray™ Accelerator LT100.In the process, the plate is assembled with a cover, followed byintroduction of 45 mL 1× phosphate buffered saline (PBS) buffer andshaking at 40 rpm for 10-20 seconds.

The washing was repeated while cells on the plate were observed andimaged between the washing steps. The left panel in FIG. 12 shows a wellwith ps2 cells after overnight incubation, before washing. The second,third and bottom panel shows a photograph taken from a same well after1^(st), 2^(nd) and 6^(th) washes. After 6^(th) wash, it was observedthat a significant portion of cells were dying, presumably due to thewashing buffer used, 1×PBS affecting the integrity of cells. Still, theloss of cells was relatively insignificant, indicating gentleness of thewashing on the cells.

In the example of washing suspension cells of multilayers, the plate maybe modified to contain 2 mm diameter of hydrophilic elements with, forexample, 1-2 mm depth (i.e., the height of the overlay is 1-2 mm).Furthermore, the washing may be modified to reduce the stress byfluidics. For example, the wash buffer is introduced and drained at alower flow rate, say 50% of the conventional flow rate and the shakingis reduced to 0-20 rpm. Instead of the reduced or the absence ofshaking, the plate may include a resting period of, for example, 20-60seconds at each washing step in order to induce natural diffusion of thereagent to the bulk wash buffer. With the increased depth and gentlerfluidics, the hydrophilic element of 2 mm diameter may be able to retainmore than 50% of cell numbers of, for example, Jurkat T cells at thedensity of 3000 cells per element, after 3 times repeated washing.

Example III

In this example, the Cell Titer96® Aqueous Non-Radioactive CellProliferation Assay (sold by Promega Corp., Madiscon, Wis., USA) isminiaturized using the grid and system of the invention.

The protocol for the Cell Titer96® Aqueous Non-Radioactive CellProliferation Assay is available in Promega's Technical Bulletin forProducts G5421, G5430, G5440, G1111, and G1112 (Rev. 5/09; Part#TB169from Promega Corp.).

As described in Example I, adherent cells are grown on a 384-elementDropArray™ plate. The adherent cells used in this example are the MCF7human breast cancer cells (commercially available from American TypeCulture Collection; Manassas, Va., USA). In this experiment, the amountof tumor necrosis factor alpha (TNFa) need to inhibit cell growth by 90%was determined by tittering the amount of TNFa added to the cells.

The cells are grown in Eagle's minimum Essential Medium (ATCC CatalogNo. 30-2003) with 0.01 mg/ml bovine insulin and 10% fetal bovine serum(“culture media”). 2 ul droplets of culture media containing MCF7 cellsare pipetted onto the elements of an apparatus (in this case, a 384element Droparray™ plate), and the plate is incubated for 24 hours at37° C. in 5° C. CO₂.

Ninety-five different concentrations of TNFa are made in culture media.A grid comprising 96 through-holes is inserted into the apparatus suchthat four elements (and four different cell populations) are within eachgrid. A standard pipet is then used to add 4 ul of each of the 95 TNFaconcentrations to each through-hole. A final 4 ul of culture media withno TNFa is added to the 96^(th) through-hole of the grid. After the 4 uldrops are delivered, the plate is gently tilted manually until the 4 uldrops are dispersed into each of the 4 elements within the through-hole.The plate is then returned to incubation for 24 hours at 37° C. in 5° C.CO₂. During incubation, the grid is left on the apparatus.

After incubation, the grid is removed and the plate washed in aDropArray™ Accelerator LT100 (commercially available from CurioxBiosystems) as described above. MTS Solution and the PMS solution fromthe CellTiter96 plate are prepared as described in Promega's TechnicalBulletin.

A different grid, comprising 384 through-holes where the through-holeshave a slightly larger diameter than the 2 mm diameter of the elementsof the DropArray™ plate is next inserted into the plate. 5 ul of theMTS/PMS solution is added into each through-hole of the grid. The plate(with inserted grid) is next incubated for 4 hours at 37° C. in 5° C.CO₂. The plate is then removed from the incubator and absorbance readimmediately at 490 nm using a standard ELISA plate reader configured for384 wells.

Using the absorbance values from the four cell populations treated withthe same amount of TNFa, the ED50 value of TNFa on MCF7 cells can bereadily determined with the degrees of confidence obtained from thisstudy that used few reagents and few cells.

Example IV

In this example, an embodiment of the plate depicted in FIG. 11 will beemployed to assess which height is useful in retaining two commonly usedsuspension cells. The optimal height will vary depending upon the celltype and specific characteristic of that cell (e.g., mass, diameter, andreaction assay being performed). The following two suspension cells (allcommercially available from the ATCC (Manassas, Va., USA)) will be used:human Jurkat T cells (ATCC No. TIB-152) and human Daudi B cells (ATCCNo. CCL-213).

In this example, three different 384 element apparatuses based on theapparatus depicted in FIG. 11 are employed. All have 384 elements of 2mm diameter each. The first apparatus has an overlay height of 0.5 mmover the surface of the elements. The second has a height of 1 mm. And,the third has a height of 2 mm.

Different numbers of Daudi and Jurkat cells are plated onto each of theapparatuses, where the same number of each cell type is plated ontoelements in the same location of each of the four apparatuses. Sinceboth Daudi and Jurkat cells express CD5 antigen at their cell surface, adetectably labeled anti-human CD5 antibody is added to each well (e.g.,the AlexFluor 700-labeled anti-human CD5 antibody sold as Catalog No.561159 by BD Biosciences, San Diego, Calif., USA). After washing theapparatuses using the cell washing process in the DropArray™ AcceleratorHT200 (Curiox Biosystems, Signapore), the amount of fluorescence isdetermined using a standard ELISA plate reader and the cells are counted(e.g., using a haemocytometer or other standard cell countingtechnique).

In this manner, the optimal apparatus (i.e., the optimal height of theoverlay) for each cell type can be determined that retains the greatestamount of cells and the lowest amount of background (i.e., unboundAlexFluor anti-CD5 antibody). Furthermore, the washing may be modifiedto reduce the stress by fluidics. For example, the wash buffer isintroduced and drained at a lower flow rate, say 50% of the conventionalflow rate and the shaking is reduced to 0-20 rpm. Instead of the reducedor the absence of shaking, the plate may include a resting period of,for example, 20-60 seconds at each washing step in order to inducenatural diffusion of the reagent to the bulk wash buffer. With theincreased depth and gentler fluidics, the hydrophilic element of 2 mmdiameter may be able to retain more than 50% of cell numbers of, forexample, Jurkat cells or Daudi cells at the density of 3000 cells perelement, after 3 times repeated washing.

While the invention has been described with particular reference to theillustrated embodiments, it will be understood that numerousmodifications thereto will appear to those skilled in the art.Accordingly, the above description, the following claims, andaccompanying drawings should be taken as illustrative of the inventionand not in a limiting sense.

What is claimed is:
 1. An apparatus for improving retention ofnon-adherent cells on a plate, the apparatus comprising: the platecomprising a number of elements having a first surface energy arrangedin an array with an overlay, on the plate, having a second surfaceenergy, the first surface energy resulting in a hydrophilic surface andthe second surface energy resulting in a hydrophobic surface, wherein: adiameter of the elements is at least 1 mm; and a height of the overlayhaving the second surface energy, which results in a hydrophobicsurface, is between 5% and 100% of the diameter of the elements; a wallcircumferential to the plate; and a removable grid insertable into theapparatus to be positioned over the plate and within the wall of theapparatus, the grid comprising dividers enclosing a number ofthrough-holes, said through-holes spaced in the grid to allow alignmentof the through-holes of the grid over the elements in the plate when thegrid is inserted into the apparatus, wherein said dividers of the gridinserted into the apparatus form sides of wells bottomed by the plateand at least one element on said plate, the grid has a surface energythat results in a hydrophobic surface, and the grid is distinct andseparate from the overlay and the wall.
 2. The apparatus of claim 1,wherein the apparatus further comprises a positioning structure adjacentto the interior of the wall so as to guide alignment of thethrough-holes of the grid over the elements when the grid is insertedinto the apparatus.
 3. The apparatus of claim 1, wherein the number ofthrough-holes in the grid is the same as the number of elements in theplate.
 4. The apparatus of claim 1, wherein the number of though-holesin the grid is smaller than the number of elements in the plate.
 5. Theapparatus of claim 4, wherein each through-hole is aligned over multipleelements in the plate.
 6. The apparatus of claim 1, wherein the gridfurther comprises baffles on the surface of the grid that touches theplate when the grid is inserted into the apparatus.
 7. The apparatus ofclaim 1, wherein the grid has the second surface energy.
 8. Theapparatus of claim 1, wherein the grid further comprises at least onestructure on the surface of the grid that does not touch the plate whenthe grid is inserted into the apparatus, said structure sized for a userto grab the grid and insert or remove the grid from the apparatus. 9.The apparatus of claim 1, wherein the grid further comprises a reservoirencompassing at least one through-hole of the grid, said reservoir onthe surface of the grid that does not touch the plate when the grid isinserted into the apparatus.
 10. The apparatus of claim 1, wherein thedividers of the grid and the wall of the apparatus are of the sameheight.
 11. The apparatus of claim 1, wherein the dividers of the gridare of a height that is higher than the height of the wall of theapparatus.
 12. The apparatus of claim 1, wherein the grid furthercomprises a lid perpendicular to the dividers of the grid attached tothe surface of the grid that does not touch the plate when the grid isinserted into the apparatus, wherein the lid covers all of thethrough-holes of the grid.
 13. The apparatus of claim 12, wherein thelid further comprises sides perpendicular to said lid, said sidesparallel to and shorter than the dividers of the grid.
 14. The apparatusof claim 13, wherein the grid further comprises baffles between thedividers and the lid.
 15. The apparatus of claim 1, wherein the heightof the overlay over the elements is between 10% and 80% of the diameterof the elements.
 16. The apparatus of claim 1, wherein the height of theoverlay over the elements is between 20% and 50% of the diameter of theelements.
 17. The apparatus of claim 1, wherein the dividers are aligneddirectly over the hydrophobic surface the overlay having the secondsurface energy resulting in the hydrophobic surface when the grid isinserted into the apparatus.
 18. The apparatus of claim 1, wherein thewall circumferential to the plate defines a reservoir and the apparatusincludes an oil within the reservoir.
 19. The apparatus of claim 18,wherein the removable grid has a weight that prevents flotation of theremovable grid on the oil within the reservoir.
 20. The apparatus ofclaim 1, wherein the diameter of the element is at least 2 mm.
 21. Theapparatus of claim 1, wherein the overlay is made ofpolytetrafluoroethylene.
 22. A method for performing multiple reactions,comprising: (a) providing (i) an apparatus for improving retention ofnon-adherent cells on a plate, the apparatus comprising the platecomprising a number of elements having a first surface energy arrangedin an array with an overlay, on the plate, having a second surfaceenergy, the first surface energy resulting in a hydrophilic surface andthe second surface energy resulting in a hydrophobic surface, wherein adiameter of the elements is at least 1 mm and a height of the overlayhaving the second surface energy, which results in a hydrophobicsurface, is between 5% and 100% of the diameter of the elements; (ii) awall circumferential to the plate; and (iii) a removable grid insertableinto the apparatus to be positioned over the plate and within the wallof the apparatus, the grid comprising dividers enclosing a number ofthrough-holes, said through-holes spaced in the grid to allow alignmentof the through-holes of the grid over the elements in the plate when thegrid is inserted into the apparatus, wherein said dividers of said gridinserted into the apparatus form sides of wells bottomed by the plateand at least one element on said plate, the grid has a surface energythat results in a hydrophobic surface, and the grid is distinct andseparate from the overlay and the wall; (b) adding a firstreagent-containing liquid through the through-holes of the grid underconditions where the first reagent in the liquid adheres to the elementson the plate; (c) adding rinsing oil to said plate in an amountnecessary to cover said plate; (d) draining excess rinsing oil from theplate resulting from step (c); (e) adding a liquid through thethrough-holes of the grid, said liquid containing a second reagentsuspected of reacting with the first reagent; (f) removing the grid fromthe apparatus; (g) washing the apparatus; and (h) detecting reaction ofthe second reagent with the first reagent.
 23. The method of claim 22,wherein the first reagent is a cell.
 24. The method of claim 23, whereinthe cell is selected from the group consisting of an adherent cell, anon-adherent cell, and a permeabilized cell.
 25. The method of claim 23,wherein the second reagent is selected from the group consisting of anagonist or an antagonist.
 26. The method of claim 22, wherein the firstreagent is a binding agent.
 27. The method of claim 26, wherein thebinding agent is selected from the group consisting of a single-strandednucleic acid molecule, an antibody, and a ligand.
 28. The method ofclaim 22 further comprising inserting the grid into the apparatusfollowing step (g).
 29. The method of claim 22, wherein step (h) isperformed using a third reagent.
 30. The method of claim 29, wherein thethird reagent is detectably labeled.